Functional genomics of breast cancer

乳腺癌的功能基因组学

• 批准号: 7733483
• 负责人: PAUL S. MELTZER
• 金额: $ 126.37万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7733483
• 关键词: Address; Adult; Archives; Behavior; Binding; Bioinformatics; Biological Assay; Biological Models; Breast Cancer Treatment; Cancer Biology; Candidate Disease Gene; Caring; Categories; Cells; Childhood; Chromatin; Chromosomal translocation; Classification; Clinical; Clinical Trials; Code; Cultured Cells; DNA; DNA Methylation; DNA Sequence; DNA copy number; Data; Development; Diagnosis; Diagnostic; Disease; Epithelial; Estrogens; Event; Exons; Fluorescent Probes; Formalin; Freezing; Functional RNA; Gene Amplification; Gene Dosage; Gene Expression; Genes; Genetic Transcription; Genetically Engineered Mouse; Genome; Genomics; Goals; Growth; Human; Human Genome; Individual; Investigation; Label; Laboratories; Lead; Learning; Left; Link; Malignant Neoplasms; Mammary gland; Measures; Methods; Methylation; Modeling; Modification; Molecular; Molecular Profiling; Mutation; Noninfiltrating Intraductal Carcinoma; Nucleic Acids; Numbers; Oligonucleotides; Paraffin Embedding; Pathologist; Pathway interactions; Phenotype; Process; Progesterone; Property; Purpose; Research; Research Personnel; Resolution; Role; Sampling; Scientist; Sequence Analysis; Single Nucleotide Polymorphism; Small RNA; Solid; Source; Specialist; Specimen; Standards of Weights and Measures; Structure; Study models; Technology; Tissues; Tumor Biology; Tumor Tissue; Variant; Work; base; cancer cell; cancer genome; chromatin immunoprecipitation; design; desire; functional genomics; genome sequencing; genome-wide analysis; improved; interest; malignant breast neoplasm; multidisciplinary; next generation; research study; sarcoma; size; transcription factor; tumor; Address; Adult; Archives; Behavior; Binding; Bioinformatics; Biological Assay; Biological Models; Breast Cancer Treatment; Cancer Biology; Candidate Disease Gene; Caring; Categories; Cells; Childhood; Chromatin; Chromosomal translocation; Classification; Clinical; Clinical Trials; Code; Cultured Cells; DNA; DNA Methylation; DNA Sequence; DNA copy number; Data; Development; Diagnosis; Diagnostic; Disease; Epithelial; Estrogens; Event; Exons; Fluorescent Probes; Formalin; Freezing; Functional RNA; Gene Amplification; Gene Dosage; Gene Expression; Genes; Genetic Transcription; Genetically Engineered Mouse; Genome; Genomics; Goals; Growth; Human; Human Genome; Individual; Investigation; Label; Laboratories; Lead; Learning; Left; Link; Malignant Neoplasms; Mammary gland; Measures; Methods; Methylation; Modeling; Modification; Molecular; Molecular Profiling; Mutation; Noninfiltrating Intraductal Carcinoma; Nucleic Acids; Numbers; Oligonucleotides; Paraffin Embedding; Pathologist; Pathway interactions; Phenotype; Process; Progesterone; Property; Purpose; Research; Research Personnel; Resolution; Role; Sampling; Scientist; Sequence Analysis; Single Nucleotide Polymorphism; Small RNA; Solid; Source; Specialist; Specimen; Standards of Weights and Measures; Structure; Study models; Technology; Tissues; Tumor Biology; Tumor Tissue; Variant; Work; base; cancer cell; cancer genome; chromatin immunoprecipitation; design; desire; functional genomics; genome sequencing; genome-wide analysis; improved; interest; malignant breast neoplasm; multidisciplinary; next generation; research study; sarcoma; size; transcription factor; tumor

A number of technologies are applied in parallel to determine the molecular profile of a given biospecimen. The majority of these technologies currently use microarray based methods, but they are rapidly being supplemented by evolving next generation DNA sequencing technologies. Several varieties of microarray are used for various purposes, but the predominant current technical approaches use synthetic oligonucleotides bound to a solid support and interrogated with labeled nucleic acids prepared from the biospecimen of interest. The power of this approach in the current embodiment of this technology is based largely on the direct connection between known genome sequence and the design of microarrays completely controlled by computational means. This allows the investigator to construct arrays of arbitrary design tailored specifically to the desired analysis and to adjust the resolution of the arrays to a remarkably fine level. Thus, for example, it is now possible to determine the expression of mRNAs exon by exon and to observe changes in gene copy number (amplification or deletion) at better than single gene resolution. Fluorescent probes prepared from any cell or tissue source of interest are then hybridized to these arrays providing a large scale high resolution view of the genome. Our recent efforts have applied this technology to pediatric and adult sarcomas. Currently we are focused on transitioning as many assays as possible to minute samples (such as may typically be collected in the course of routine clinical care) and formalin fixed paraffin embedded (FFPE) specimens. The ability to work with FFPE samples is particularly important when one considers the potential to transition discoveries made in the course of this work to clinical care where FFPE based methods are the standard method of stabilizing biospecimens in the clinical laboratory. Of importance we have demonstrated that it is possible to determine the methylation status of more than 1500 CpGs in parallel on hundreds of samples with results which match those obtained from frozen specimens. This opens vast existing archives of FFPE samples to investigation. We now routinely obtain excellent copy number data from FFPE samples as well. We are particularly interested in the role of specific transcription factors in determining breast cancer phenotypes and have been investigating these through chromatin immunoprecipitation combined with microarray or sequencing analysis. We have recently investigated the problem of grading ductal carcinoma in situ (DCIS). Pathologists are able to grade DCIS into high or low grade categories, but are left with a large number of cases which are intermediate in grade. We have demonstrated that it is possible to place these cases in either the high or low grade categories by expression profiling. This establishes a binary classification of DCIS which has the potential to improve individual diagnosis and to be used to stratify clinical trials.

并行应用许多技术来确定给定的生物测量的分子谱。这些技术中的大多数目前都使用基于微阵列的方法，但是通过不断发展的下一代DNA测序技术来迅速补充它们。几种微阵列用于各种目的，但是主要的当前技术方法使用合成寡核苷酸结合到固体支持并用根据感兴趣的生物测量制备的标记的核酸进行审查。 该技术在该技术的当前实施方案中的力量主要基于已知基因组序列与完全由计算手段完全控制的微阵列设计之间的直接连接。这使研究人员可以构建专门针对所需分析的任意设计的阵列，并将阵列的分辨率调整到非常良好的水平。因此，例如，现在可以通过外显子确定mRNA外显子的表达，并观察到基因拷贝数（扩增或删除）的变化比单个基因溶液更好。然后将从任何细胞或组织来源制备的荧光探针与这些阵列杂交，从而提供了大规模的基因组高分辨率视图。我们最近的努力将这项技术应用于儿科和成人肉瘤。目前，我们专注于过渡到尽可能多的分量样品（例如通常在常规临床护理过程中收集）和福尔马林固定石蜡嵌入（FFPE）标本。当人们认为在这项工作中进行过渡到临床护理中的过渡发现的潜力是，基于FFPE的方法是稳定临床实验室中的生物测量的标准方法时，使用FFPE样品的能力尤为重要。重要的是，我们已经证明，可以在数百个样品上并行确定超过1500个CPG的甲基化状态，并与从冷冻样本获得的结果相匹配。这为FFPE样品的大量档案打开了调查。现在，我们通常还从FFPE样本中获得出色的拷贝数数据。我们对特定转录因子在确定乳腺癌表型中的作用特别感兴趣，并一直通过染色质免疫沉淀与微阵列或测序分析一起研究它们。我们最近研究了原位导管癌的分级问题（DCIS）。病理学家能够将DCIS评级为高或低级类别，但仍有大量中间的病例。我们已经证明，可以通过表达分析将这些案例置于高级或低级类别中。这建立了DCI的二元分类，该分类有可能改善个体诊断并用于对临床试验进行分层。